Research workbench
The human nucleosome structure containing the histone variant H3.3
Analyse The human nucleosome structure containing the histone variant H3.3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AV2
- Type
- protein + DNA
- Length
- 1,044 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.3; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; 146-mer DNA
- UniProt
- P84243, P62805, P04908, P06899
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 9 distinct chains · 64% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.3 | protein | 97 | 63% helix, 4% strand | P84243 |
| B | Histone H4 | protein | 78 | 63% helix, 8% strand | P62805 |
| C | Histone H2A type 1-B/E | protein | 105 | 57% helix, 6% strand | P04908 |
| D | Histone H2B type 1-J | protein | 94 | 73% helix, 4% strand | P06899 |
| E | Histone H3.3 | protein | 98 | 64% helix, 4% strand | P84243 |
| F | Histone H4 | protein | 84 | 60% helix, 7% strand | P62805 |
| G | Histone H2A type 1-B/E | protein | 104 | 56% helix, 6% strand | P04908 |
| H | Histone H2B type 1-J | protein | 92 | 76% helix, 4% strand | P06899 |
| I, J | 146-mer DNA | dna | 146 | — | — |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 718 | 0.80 | 0.84 | 66 | empty |
| 2 | 519 | 0.77 | 0.84 | 57 | empty |
| 3 | 388 | 0.76 | 0.86 | 49 | empty |
| 4 | 564 | 0.69 | 0.79 | 42 | empty |
| 5 | 647 | 0.67 | 0.77 | 48 | empty |
Interfaces
35 interfaces between chains.
- I–J · 6452 Ų buried · 531 hydrogen bonds · nucleic-nucleic
- E–F · 2616 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 2610 Ų buried · 30 hydrogen bonds · protein-protein
- G–H · 2564 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2514 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3AV2 · The human nucleosome structure containing the histone variant H3.3 · the same entry in another collection · chain J against J, TM-score 1.00
- P84243 · AlphaFold monomer V2.0 prediction for histone H3.3 (P84243) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P06899 · AlphaFold monomer V2.0 prediction for histone H2B type 1-J (P06899) · a predicted model of the same protein · chain H against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P84243
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt P06899
- Elsewhere: RCSB PDB 3AV2 · PDBe 3AV2 · UniProt P84243 · UniProt P62805 · UniProt P04908 · UniProt P06899
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